Package: iPAC

Version: 1.22.0

Command: rm -rf iPAC.buildbin-libdir iPAC.Rcheck && mkdir iPAC.buildbin-libdir iPAC.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=iPAC.buildbin-libdir iPAC_1.22.0.tar.gz >iPAC.Rcheck\00install.out 2>&1 && cp iPAC.Rcheck\00install.out iPAC-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=iPAC.buildbin-libdir --install="check:iPAC-install.out" --force-multiarch --no-vignettes --timings iPAC_1.22.0.tar.gz

StartedAt: 2018-04-12 00:52:18 -0400 (Thu, 12 Apr 2018)

EndedAt: 2018-04-12 00:58:53 -0400 (Thu, 12 Apr 2018)

EllapsedTime: 394.5 seconds

RetCode: 0

Status:  OK

CheckDir: iPAC.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf iPAC.buildbin-libdir iPAC.Rcheck && mkdir iPAC.buildbin-libdir iPAC.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=iPAC.buildbin-libdir iPAC_1.22.0.tar.gz >iPAC.Rcheck\00install.out 2>&1 && cp iPAC.Rcheck\00install.out iPAC-install.out  &&  C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=iPAC.buildbin-libdir --install="check:iPAC-install.out" --force-multiarch --no-vignettes --timings iPAC_1.22.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/iPAC.Rcheck'
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'iPAC/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'iPAC' version '1.22.0'
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking whether package 'iPAC' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* loading checks for arch 'i386'
** checking whether the package can be loaded ... OK
** checking whether the package can be loaded with stated dependencies ... OK
** checking whether the package can be unloaded cleanly ... OK
** checking whether the namespace can be loaded with stated dependencies ... OK
** checking whether the namespace can be unloaded cleanly ... OK
* loading checks for arch 'x64'
** checking whether the package can be loaded ... OK
** checking whether the package can be loaded with stated dependencies ... OK
** checking whether the package can be unloaded cleanly ... OK
** checking whether the namespace can be loaded with stated dependencies ... OK
** checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... NOTE
Packages in Depends field not imported from:
  'Biostrings' 'gdata' 'multtest' 'scatterplot3d'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
Plot.Protein.Linear: no visible global function definition for
  'heat.colors'
Plot.Protein.Linear: no visible global function definition for 'gray'
Plot.Protein.Linear: no visible global function definition for
  'topo.colors'
Plot.Protein.Linear: no visible global function definition for
  'cm.colors'
Plot.Protein.Linear: no visible global function definition for 'par'
Plot.Protein.Linear: no visible global function definition for 'plot'
Plot.Protein.Linear: no visible global function definition for 'rect'
Plot.Protein.Linear: no visible global function definition for 'text'
SetTextContrastColor: no visible global function definition for
  'col2rgb'
calcorder: no visible global function definition for 'dist'
calcorder: no visible global function definition for 'cmdscale'
difforder0: no visible global function definition for 'pbinom'
difforder0: no visible global function definition for 'dmultinom'
difforder1: no visible global function definition for 'dmultinom'
get.AlignedPositions: no visible global function definition for
  'PhredQuality'
get.AlignedPositions: no visible global function definition for
  'pairwiseAlignment'
get.AlignedPositions: no visible global function definition for 'start'
nmc: no visible global function definition for 'pbeta'
nmc: no visible global function definition for 'mt.rawp2adjp'
plotLinear: no visible global function definition for 'pdf'
plotLinear: no visible global function definition for 'scatterplot3d'
plotLinear: no visible global function definition for 'dev.off'
plotLinear: no visible global function definition for 'dev.copy2pdf'
plotMDS: no visible global function definition for 'pdf'
plotMDS: no visible global function definition for 'scatterplot3d'
plotMDS: no visible global function definition for 'dev.off'
plotMDS: no visible global function definition for 'dev.copy2pdf'
Undefined global functions or variables:
  PhredQuality cm.colors cmdscale col2rgb dev.copy2pdf dev.off dist
  dmultinom gray heat.colors mt.rawp2adjp pairwiseAlignment par pbeta
  pbinom pdf plot rect scatterplot3d start text topo.colors
Consider adding
  importFrom("grDevices", "cm.colors", "col2rgb", "dev.copy2pdf",
             "dev.off", "gray", "heat.colors", "pdf", "topo.colors")
  importFrom("graphics", "par", "plot", "rect", "text")
  importFrom("stats", "cmdscale", "dist", "dmultinom", "pbeta", "pbinom",
             "start")
to your NAMESPACE file.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
ClusterFind         67.53   0.36   68.07
get.Positions       16.58   4.78   22.27
nmc                 15.44   0.00   15.43
Plot.Protein.Linear  5.05   0.36    5.58
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
ClusterFind         80.31   0.69   81.17
get.Positions       32.11   7.28   40.11
nmc                 19.16   0.01   19.17
Plot.Protein.Linear  5.23   0.48    5.81
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  'C:/Users/biocbuild/bbs-3.6-bioc/meat/iPAC.Rcheck/00check.log'
for details.

install for i386

* installing *source* package 'iPAC' ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'iPAC'
    finding HTML links ... done
    ClusterFind                             html  
    KRAS.Mutations                          html  
    PIK3CA.Mutations                        html  
    Plot.Protein.Linear                     html  
    get.AASeq                               html  
    get.AlignedPositions                    html  
    get.Positions                           html  
    get.Remapped.Order                      html  
    get.SingleLetterCode                    html  
    iPAC-package                            html  
    nmc                                     html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'iPAC' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'iPAC' as iPAC_1.22.0.zip
* DONE (iPAC)
In R CMD INSTALL
In R CMD INSTALL